This grant is submitted in response to the Program Announcement Tools for Genetic and Genomic Studies in Emerging Model Organisms. I propose to construct a 300-marker linkage map in the ascidian, Ciona savignyi, that is fully integrated with what will become the annotated high quality genome reference sequence. This map will not only aid in the cloning of mutations, but also in achieving the long range contiguity in the C. savignyi reference sequence that will be needed to efficiently perform whole genome scans for induced or naturally occurring mutations. In addition to the genome-wide map, high-resolution fine- scale mapping in regions of uncertain sequence assembly will be performed to resolve ambiguities in the C. savignyi genome reference sequence. The map, along with a database of thousands of potentially polymorphic markers distributed across the genome, will be made available to the community. Ascidians are among the simplest chordates, yet their fundamental developmental mechanisms are structurally and molecularly conserved with those of vertebrates. Despite the high level of conservation, ascidian genomes are comparable in size to Drosophila's (about 180 Mb), thus exhibiting experimentally advantageous genomic simplicity. Further, ascidians have many attractive embryological and experimental features that facilitate studies of gene regulation during development. Over the past few years, C. savignyi has been developed as a genetic model organism, with mutants readily obtainable from wild populations or by mutagenesis. The genetic map, the markers, and the long-range contiguity of the genome assembly are the missing, critically important, resources to establish C. savignyi as a full-fledged genetic and genomic model organism. Ciona savignyi and its sister species, Ciona intestinalis, are uniquely informative with regards to the mechanisms of chordate embryonic development. Fundamental as well as specific features of embryonic development and gene regulation are conserved between humans and these chordates. Insights into the molecular mechanisms of regulation and development using Ciona as a model are highly effective and relevant to the homologous processes in human.